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Series GSE49313 Query DataSets for GSE49313
Status Public on Sep 15, 2013
Title eRNAs Promote Transcription by Establishing Chromatin Accessibility at Defined Genomic Loci
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary Transcription factors and DNA regulatory binding motifs are fundamental components of the gene regulatory network (GRN). Here, by using genome-wide occupancy profiling of master regulators of MyoGenesis (MyoD and MyoGenin), we show their extensive occupancy in the extragenic enhancer regions coinciding with RNA synthesis (i.e. eRNA). In particular, multiple regions coding for eRNAs were observed within regulatory region of MYOD1, including previously characterized Distal Regulatory Regions (DRR) and Core Enhancer (CE). While CERNA enhanced RNA polymerase II (PolII) occupancy and transcription at MYOD1, DRRRNA acted in trans to activate the downstream MyoGenic GRN. The deployment of transcriptional machinery to appropriate loci is contingent on chromatin accessibility, a rate-limiting step preceding PolII assembly. By nuclease sensitivity assay, we show that eRNAs increase genomic access to the transcriptional complex at defined regulatory regions. In conclusion, our data suggest eRNAs establish a cell-type-specific transcriptional circuitry by directing chromatin-remodeling events.
Overall design Examination of MyoD and MyoG binding events and production of RNA at the enhancer sites during myogenic differentiation. We performed RNAi against enhancer-derived RNA (DRRi) which resulted in reduction of chromatin accessiblity and RNA polymerase II occupancy at defined regulatory elements. In complementary experiments, overexpression of DRR-RNA (pHAN_DRR1.2) resulted in early activation of MyoG. GFPi and GFP overexpression (pHAN_GFP) were used as control in these experiments, respectively.
Contributor(s) Mousavi K, Zare H, Dell'Orso S, Grontsved L, Gutierrez-Cruz G, Derfoul A, Hager GL, Sartorelli V
Citation(s) 23993744
Submission date Jul 29, 2013
Last update date May 15, 2019
Contact name Hossein Zare
Organization name NIH
Street address 5o South Dr #1347
City Bethesda
ZIP/Postal code 20892
Country USA
Platforms (2)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (11)
GSM1197184 MB_MyoD_ChIPseq
GSM1197185 MT_MyoD_ChIPseq
GSM1197186 MT_MyoG_ChIPseq
BioProject PRJNA213621
SRA SRP028299

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Supplementary file Size Download File type/resource
GSE49313_DRRi_GFPi_cds_exp.diff.txt.gz 909.1 Kb (ftp)(http) TXT
GSE49313_PhanDRR1.2_PhanGFP_cds_exp.diff.txt.gz 922.5 Kb (ftp)(http) TXT
GSE49313_RAW.tar 1.7 Gb (http)(custom) TAR (of BED, BIGWIG, WIG)
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Raw data are available in SRA
Processed data provided as supplementary file

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